Entity framework, problems updating related objects

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CurrentValues.SetValues only updates scalar properties but no related entities, so you must do the same for each related entity:

public Foo Edit(Foo newFoo)
{
    var dbFoo = context.Foo
                       .Include(x => x.SubFoo)
                       .Include(x => x.AnotherSubFoo)
                       .Single(c => c.Id == newFoo.Id);

    context.Entry(dbFoo).CurrentValues.SetValues(newFoo);
    context.Entry(dbFoo.SubFoo).CurrentValues.SetValues(newFoo.SubFoo);
    context.Entry(dbFoo.AnotherSubFoo).CurrentValues.SetValues(newFoo.AnotherSubFoo);

    context.SaveChanges();

    return newFoo;
}

If the relationship could have been removed altogether or have been created you also need to handle those cases explicitly:

public Foo Edit(Foo newFoo)
{
    var dbFoo = context.Foo
                       .Include(x => x.SubFoo)
                       .Include(x => x.AnotherSubFoo)
                       .Single(c => c.Id == newFoo.Id);

    context.Entry(dbFoo).CurrentValues.SetValues(newFoo);
    if (dbFoo.SubFoo != null)
    {
        if (newFoo.SubFoo != null)
        {
            if (dbFoo.SubFoo.Id == newFoo.SubFoo.Id)
                // no relationship change, only scalar prop.
                context.Entry(dbFoo.SubFoo).CurrentValues.SetValues(newFoo.SubFoo);
            else
            {
                // Relationship change
                // Attach assumes that newFoo.SubFoo is an existing entity
                context.SubFoos.Attach(newFoo.SubFoo);
                dbFoo.SubFoo = newFoo.SubFoo;
            }
        }
        else // relationship has been removed
            dbFoo.SubFoo = null;
    }
    else
    {
        if (newFoo.SubFoo != null) // relationship has been added
        {
            // Attach assumes that newFoo.SubFoo is an existing entity
            context.SubFoos.Attach(newFoo.SubFoo);
            dbFoo.SubFoo = newFoo.SubFoo;
        }
        // else -> old and new SubFoo is null -> nothing to do
    }

    // the same logic for AnotherSubFoo ...

    context.SaveChanges();

    return newFoo;
}

You eventually also need to set the state of the attached entities to Modified if the relationship has been changed and the scalar properties as well.

Edit

If – according to your comment – Foo.SubFoo is actually a collection and not only a reference you will need something like this to update the related entities:

public Foo Edit(Foo newFoo)
{
    var dbFoo = context.Foo
                       .Include(x => x.SubFoo)
                       .Include(x => x.AnotherSubFoo)
                       .Single(c => c.Id == newFoo.Id);

    // Update foo (works only for scalar properties)
    context.Entry(dbFoo).CurrentValues.SetValues(newFoo);

    // Delete subFoos from database that are not in the newFoo.SubFoo collection
    foreach (var dbSubFoo in dbFoo.SubFoo.ToList())
        if (!newFoo.SubFoo.Any(s => s.Id == dbSubFoo.Id))
            context.SubFoos.Remove(dbSubFoo);

    foreach (var newSubFoo in newFoo.SubFoo)
    {
        var dbSubFoo = dbFoo.SubFoo.SingleOrDefault(s => s.Id == newSubFoo.Id);
        if (dbSubFoo != null)
            // Update subFoos that are in the newFoo.SubFoo collection
            context.Entry(dbSubFoo).CurrentValues.SetValues(newSubFoo);
        else
            // Insert subFoos into the database that are not
            // in the dbFoo.subFoo collection
            dbFoo.SubFoo.Add(newSubFoo);
    }

    // and the same for AnotherSubFoo...

    db.SaveChanges();

    return newFoo;
}

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